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@brainglobe

BrainGlobe

Interoperable Python-based tools for computational neuroanatomy

The BrainGlobe Initiative exists to facilitate the development of interoperable Python-based tools for computational neuroanatomy.

We have three aims:

  • Develop specialist software for specific analysis and visualisation needs, such as cellfinder and brainrender.

  • Develop core tools to facilitate others to build interoperable tools in Python, e.g. the BrainGlobe Atlas API.

  • Build a community of neuroscientists and developers to share knowledge, build software and engage with the scientific, and open-source community (e.g. by organising hackathons).

For more details please see the website. For help using the tools please contact us via the image.sc forum and to get in touch with us about contributing, please use the BrainGlobe Zulip chat.

Development is currently led by the Neuroinformatics Unit at the Sainsbury Wellcome Centre and the Gatsby Computational Neuroscience Unit.

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  1. brainglobe-atlasapi brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    Python 187 72

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 673 108

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 231 81

  4. brainreg brainreg Public

    Automated 3D brain registration with support for multiple species and atlases.

    Python 150 37

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 37 12

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 52 28

Repositories

Showing 10 of 59 repositories
  • brainglobe/brainglobe-data-api-connectivity's past year of commit activity
    Python 2 BSD-3-Clause 1 18 2 Updated Oct 2, 2026
  • brainglobe-data-api-connectivity-frontend Public

    A web frontend for browsing brain connectivity data.

    brainglobe/brainglobe-data-api-connectivity-frontend's past year of commit activity
    Python 0 BSD-3-Clause 0 2 0 Updated Oct 2, 2026
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io's past year of commit activity
    Python 14 CC-BY-4.0 32 61 5 Updated Oct 2, 2026
  • brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    brainglobe/brainglobe-heatmap's past year of commit activity
    Python 52 MIT 27 9 3 Updated Oct 2, 2026
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi's past year of commit activity
    Python 187 BSD-3-Clause 72 275 (1 issue needs help) 20 Updated Oct 2, 2026
  • brainglobe-napari-io Public

    Read and write files from the BrainGlobe neuroanatomy suite

    brainglobe/brainglobe-napari-io's past year of commit activity
    Python 15 BSD-3-Clause 5 3 0 Updated Sep 30, 2026
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder's past year of commit activity
    Python 231 BSD-3-Clause 81 76 (5 issues need help) 21 Updated Sep 30, 2026
  • brainrender-napari Public

    A napari plugin to render BrainGlobe atlases and associated data as layers.

    brainglobe/brainrender-napari's past year of commit activity
    Python 24 BSD-3-Clause 22 36 (1 issue needs help) 5 Updated Sep 30, 2026
  • brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    brainglobe/brainrender's past year of commit activity
    Python 673 BSD-3-Clause 108 10 0 Updated Sep 30, 2026
  • brainglobe-workflows Public

    Workflows that utilise BrainGlobe tools to perform data analysis and visualisation.

    brainglobe/brainglobe-workflows's past year of commit activity
    Python 12 BSD-3-Clause 10 32 (1 issue needs help) 0 Updated Sep 30, 2026